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1 Summary

There are two parts to creating this layer:

  1. Data prep to get raw data into the correct format:
    • Aggregate monthly values for aragonite saturation state to an annual mean value per cell, for baseline decade and current study period.
    • Clip rasters to extents of OHIBC region, and reproject into BC Albers projection.
    • Determine baseline by calculating decadal mean for 1880-1889.
  2. Creating the pressure layers for OHIBC:
    • Determine change in aragonite saturation state since baseline for each year of study period (2005-2014)
    • Rescale to values from 0 - 1.
    • Interpolate to coastline at 1 km resolution.

This process is completed entirely within this script.

2 Updates

Not applicable.

3 Data

Raw data was provided by Woods Hole on December 16, 2014. This data is an update to the work done by Feely et al. (2009).

4 Methods

4.1 Data Prep

4.1.1 Read raw data

Raw data is read in for 1880 - 1889 and 2005 - 2014 datasets. Latitude, longitude, and aragonite saturation state \(\Omega\) are extracted for each year in each dataset. Land cells are set to NA.

Range of \(\Omega_{1880-1889}\) for global dataset: 0.073 - 4.961.

Range of \(\Omega_{2005-2014}\) for global dataset: 0.071 - 4.451.

4.1.2 Convert raw global data to OHIBC region data

The raw data, in WGS84 coordinate ref system, is rasterized, clipped down to a bounding box around the OHIBC region, and reprojected into BC Albers projection. This data is then resampled to 1 km resolution using nearest neighbor method.

The resulting raster layers (in rasterBrick format) include annual means for each coarse cell (approx 1 degree, from original resolution) for each year in the dataset. The two decades (1880-1889 and 2005-2014) are assigned to two separate rasterBricks.

4.1.3 Calculate baseline

Determine the mean cell value across the entire decade from 1880-1889, as a baseline for ocean aragonite saturation levels.

4.2 Rescale values as pressures

Baseline aragonite saturation state \(\Omega_{base}\) is based upon the decadal average from 1880-1889.

Deviation from aragonite saturation state is determined for each year in the study period:

\[\Delta \Omega_{year} = \frac{(\Omega_{base} - \Omega_{year})}{(\Omega_{base} - 1)}\]

Note that current is subtracted from the baseline; this way, a reduction in \(\Omega\) becomes a positive pressure value. It is then normalized by the current mean state; so a decrease in \(\Omega\) while the current state is high indicates less pressure than the same decrease when the current state is near 1.

\(\Delta \Omega_{year}\) is then modified to account for increases in aragonite saturation state (pressure = 0) and arag sat state less than 1 (pressure = 1).

4.2.1 Interpolate layer to coastline at 1 km

Now that \(\Delta \Omega_{year}\) has been determined at a 1 degree cell scale, we interpolate that to the coastlines to fill NAs. Using raster::interpolate(), we select a random sample of points from the \(\Delta \Omega_{year}\) raster (for speed and memory) and apply the thin plate spline model (fields::Tps()).

4.3 Calculate mean pressure by region by year

Using 1000 m region ID raster to run zonal statistics on the pressures layers (within brick or separately?) we can calculate the regional average pressures for each year of study, and save as a .csv.

4.4 Smooth annual pressures with running average

For each study year, calculate a running average of pressure score for each region, using the study year and the prior X number of years to determine the mean pressure.

5 Provenance

Provenance summary for run 3 (442fe33): standard run (Tue May 3 15:50:18 2016)
file_name file_dir filetype uncomm_chgs commit_hash
cesm_co2sys_1880-1889.nc /Volumes/ohi/git-annex/globalprep/prs_oa/v2015/input input TRUE NA
cesm_co2sys_2005-2014.nc /Volumes/ohi/git-annex/globalprep/prs_oa/v2015/input input TRUE NA
oa_rescaled_2005-2014_2000pts.tif /Users/ohara/github/ohibc/prep/pressures/v2016/output/oa input FALSE 6fac363
ohibc_rgn_raster_1000m.tif /Users/ohara/github/ohibc/prep/regions input FALSE c474446
ohibc_rgn_wgs84.shp /Users/ohara/github/ohibc/prep/regions input FALSE b014927
ohibc_rgn.shp /Users/ohara/github/ohibc/prep/regions input FALSE b4848d1
rbrick_a18_1km_raw.tif /Users/ohara/github/ohibc/prep/pressures/v2016/int/oa input FALSE 10da874
rbrick_a20_1km_raw.tif /Users/ohara/github/ohibc/prep/pressures/v2016/int/oa input FALSE 10da874
oa_rgn_pressures.csv /Users/ohara/github/ohibc/prep/pressures/v2016/output/oa output FALSE b687ba7
pressures_oa_prep.Rmd /Users/ohara/github/ohibc/prep/pressures/v2016/. parent_script TRUE ec2b37a
pressures_lyr_fxns.R /Users/ohara/github/ohibc/prep/pressures/v2016 sourced_script FALSE 5f6534a
rast_tools.R /Users/ohara/github/ohibc/src/R sourced_script FALSE 61df74f